Doctor Who AU
by NotsoSmartguy
Summary: In an alternative universe version of the story we know teenager Clara Oswald befriends the Doctor a time traveling alien from the planet Gallifrey. Together these 2 young people start the adventure of a lifetime.
1. Clara

Doctor Who AU story 1: Clara

Clara Oswald has had a rough 1st day of High School. Being the new kid in town was never easy. Getting bullied by the popular girls, getting crap for not doing a summer book report she didn't even know about, and getting detention for texting in class. There were only 2 other people the detection room with Mr. Malloy the Teacher and another new kid. He had caucasian had blonde hair, big ears, and a leather jacket.

"Psst" he says " do you have any protoplasmic stabilizers?"

"What?"

"What? You never heard protoplasmic stabilizers? I thought you humans were more advanced than this? How am I supposed to escape this _Detention?_ " He replied.

"You don't escape you wait and they let you go, now shut up before we get in trouble."

"Jeez you're bossy. You gotta name?"

"Clara Oswald"

"Call me John Smith" the kid said as he stretched out his hand for a hand shake.

Clara thought he was really weird but in a cute kind of way and she shook his hand but didn't fully trust him yet. But something pricked her hand when they shook hands.

"Ow did pluck me with a needle?" she said a bit annoyed

"Relax now you see things like I do" as he pointed to Mr. Malloy

A scared look came over Clara's face as what she thought was her teacher was actually a monster. He was a treelike creature in a humanoid shape.

"They're called the Root" John said "they are a plant like race that secretly infiltrated the school looking for something."

The 2 of them started running as the monster followed them

"What are they looking for?" Clara asked.

"Something called the seed of conversion, it will give them the power to terraform earth into a world they can inhabit"

"You know where it is?"

"Yep" John smirks as he takes a small ruby stone out of his pocket. "I found it 1st and have kept it hidden from them"

"So do you have an actual plan or are we just going to keep running?" Clara asked panicking.

" of course I always have a plan. We just need to make it back to my ship, the Tardis."

John lead Clara to the what looked like an old Police Box

"Come on in" John said

Clara had really no choice and entered the box finding the very unexpected.

"It's much bigger on the inside." she said, shocked.

John starts speaking as he starts pressing some buttons on the console in the center of the room "Here's the short version, I am called the Doctor, I am a Timelord from the planet Gallifrey I am 57 years old, this is the the TARDIS short for Time and Relative Dimensions in Space, it's my ship and my home. Any questions?"

"I'm pretty sure that covers everything." She replied

"Good now keep just keep quiet and let me work." the Doctor said sternly. " Your voice is really annoying and I need to concentrate"

"well I guess they don't teach you basic social skills where you're from." Clara replied, surprised with how rude he was to her "What are you doing anyway."

"Trying to connect into their hive like mind via this seed. All of their technology is actually organic and connected to them via a telepathic link." the Doctor said as he hooked up the seed to the tardis via a cable.

The Doctor continued to get more and more frustrated as he just couldn't get it to work. Things got even worse when the Root began attempting to gain entry to the Tardis by breaking down the tardis walls.

"Doctor do you think you could hurry this up" Clara said " I really don't feel like dying today."

"It's not working for some reason!"

Clara half heartedly suggested "Maybe you put it in Backwards".

"Don't be ridiculous I would never make such a stupid mistake" he scoffed in a patronizing way "unless…"

He did exactly as she said and a miracle occurred….. he managed gain the connection needed to do what needs to be done

"I can't believe that actually worked" the Doctor said in shock "now time to save this."

As Clara watched the Doctor swaggered his way out of the Tardis and made his presence known to the root.

"Attention worthless weeds" He roared " I am the Doctor ,Timelord of Gallifrey here to deliver a message. Now that I have complete control of your hive minds I want you to return to your planets of origin never to return. I also want you to send a message to all other races in the universe that is they which to harm this Planet, anytime, anyplace I will be there to stop them and I won't be so merciful next time."

And with that they all vanished Clara made her way out of the Tardis.

"Well Miss Oswald it appears I am in your debt."

" Your not gonna erase my memory or anything right?" she asked

"Nah if you tell anyone I'll just go back in time and make sure you were never even born" the Doctor replied Smugly

Clara had a terrified expression on her face when he said those words.

"Relax I am only kidding"

"Well I better get home." she said "Will I ever see you again."

" At school? Nah, I am much too intelligent for your pathetic school education" he said with a hint of superiority "But I do owe you a trip so we will meet again so you can collect. Besides your not bad for a human."

As they waved bye to eachother and the Tardis dematerialized they both couldn't wait to meet again. But unbenounced to them a mysterious figure watch them from afar.

"I can't believe he said he was a Timelord" The figure scoffed "He always did love to tell tall tales to stroke his ego."

 **Author's Note : Hey guys this was just something fun I came up with since Doctor Who series 9 is awesome. I love Alternative Universe comics like Marvel's ultimate universe comics or DC's Earth one Graphic Novels and figured I'd give DW a similar treatment. Different takes on very familiar ideas. This Doctor is kinda of an Amalgamation 1, 3, 6, and 9 personality and look wise. He is very young, arrogant, and kinda egotistical but he means well. I won't go much into his back story unitil later stories. What do you think so far? Let me know in via a review**


	2. Shadows of Fear Part 1

Doctor Who AU

Shadows of fear part one

Clara sat a a lunch table all by herself and was kind of lonely and feeling alone. Most of the bullies still gave her trouble but none worse than Rose Tyler. For some reason she made Clara a target.

Rose saunters over to Clara, whose nose was in a book, and slams her hands on the table.

"Hey you. What do you think you're doing?" Rose leans in close to Clara's face. Closing her book Clara peeks up from under her bangs that sweep across her face.

"Erm...I'm sorry...reading?"

"This is my table. Get lost." Rose circles Clara, trapping her in her seat. "Who do you think you are? Huh? Waltzing in here with your know it all attitude and your stupid eyes. You don't belong here!"

Rose grabs the book from Clara's flustered hands and opens the cover.

"What is this? Do you collect leaves?" Rose holds up a withered brownish orange leaf and shows it to the others with a malicious grin.

Clara leaps up to grab the book but stumbles over the chair leg and lands on her hands. Rose and her friends laugh. With a thud, Clara's book lands flatly on her back, knocking the wind out of her heart racing and tears running down her face, Clara scrambles to gather her things.

Rose kneels down to Clara's ear and whispers,

"I am the leader of this pack. And believe me when I say you are in for a world of pain."

Rose straightens herself and towers over Clara with a wrathful glare. Wiping the tears from her cheeks, Clara brushes herself off and heads to the bathroom. Rose and the other girls giggle and smirk. Clara picks up her pace and sharply turns the corner, bumping into someone, dropping her juice box. Clara doesn't seem to notice and starts running down the corridor. She makes her way into a stall and turns the latch. For a minute, she is left in peace and quiet, holding back sobs and trying to catch her breath.

"I've got it all under control." She whispers to herself in hopes that sheer will can make it so.

A moment later, the bathroom door opens. Clara freezes. She jumps onto the toilet to hide her presence from the incomer.

"Hey you alright?" a friendly voice from the asked concerned. "I say what they did to you. I want you to know if you need someone to talk to I'm here"

Clara stayed quiet, trying to get herself together.

"My name is Martha Jones," she says as she slips a piece of paper under the door "text me later or something."

After that Martha Jones leaves hoping she made a difference. Clara picks up the paper and smiles a little bit feeling happy knowing she has someone else out there who cares.

The rest of the day went a lot better. Classes went well and she didn't get detention this time. As she walked home a familiar box materialized in front of her and a familiar face popped out.

"Need a lift?" the Doctor asked in a joking way.

"What are you doing here?" Clara asked " Better yet how do you even know I am here?"

"One I owed you a ride remember? And two that those nanites in your system from our last encounter are traceable."

" Figures," she says as she rolls her eyes. "can you take me home in this thing?"

"Of course, but don't you want to travel anywhere else first?" the Doctor asked " anywhere in time and space remember?"

Clara enters the Tardis again this time she actually can take it in since she's not on the run from monsters this time. However she did notice it seemed brighter, more homey than last time, like he was trying to make her feel at home. She noticed a change in him aswell like he was excited to have someone to talk to.

"you seem different, Did you do something with your hair?" Clara asked jokingly

With a half amused smile the Doctor Responds, "So where do you want to go?"

Clara thought long and hard about where she wanted to go. Maybe somewhere in the past? The future? Maybe someplace with a great view. And then it came to her…..

"Somewhere awesome," she said with an enthusiastic smile

The Doctor saw the look on her face and it almost brought some warmth to his hearts. He had been alone for along time and it was nice to have someone to talk to. He would never admit it though. He set the coordinates for a personal favorite spot of his and the Tardis did it's thing.

They had landed at their location and the 2 exited the tardis eager to see what's out there.

"Behold Ms. Oswald the Eternal Forest of Xetar," the Doctor shouted so loud there was an echo.

Clara is blown away by what she is seeing, an entire beautiful forest world. It was filled with plants that she had never seen before. As she look around she noticed the Doctor looked kinda worried about something.

"What's wrong?" Clara asked the Doctor.

"It's just that there's usually more people here." the Doctor said perplexed.

Just then a person in a yellow hazmat suit started coming towards them.

"Hello!" the Doctor shouted "Do you know what the Hell is going on?"

As the Doctor looked down he look in horror at the sight of 2 shadows.

"Oh No" The Doctor said "Clara get back into the Tardis and don't come out till I say so."

"Doctor what's going on?" Clara asked concerned.

As the Hazmat Suited person it's revealed the person's face was nothing but a skull, picked clean of all flesh and blood.


End file.
